Reference files for analysis of TE transcription in African Turquoise Killifish

Name: Reference files for analysis of TE transcription in African Turquoise Killifish
Creator: figshare
Published: 2021-10-05 23:19:41
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DataCite Commons2021-10-05 更新2024-07-28 收录

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README - Transposable Element Differential Expression Analysis Protocol from RNA-seq Data########################### Supplied reference files - Reference genome sequence, predicted RNA sequences and genome annotations (GCA_014300015.1; 2020 genome) These files are publicly available at: https://www.ncbi.nlm.nih.gov/bioproject/PRJNA599375/ GCA_014300015.1_MPIA_NFZ_2.0_genomic.fna GCA_014300015.1_MPIA_NFZ_2.0_genomic.gtf GCA_014300015.1_MPIA_NFZ_2.0_rna_from_genomic.fna - FishTEDB sequences for N. furzeri transposons This file can be obtained at: http://www.fishtedb.org/project/species-detail?species=Nothobranchius+furzeri Nothobranchius_furzeri_FishTEDB_TEs.fa - Modified reference files including TE sequences/annotations for * kallisto/transcriptome based method: GCA_014300015.1_MPIA_NFZ_2.0_rna_from_genomic_WithFishTEDBv4.fasta * STAR/genome based method: GCA_014300015.1_MPIA_NFZ_2.0_genomic_WithFishTEDBv4.fasta GCA_014300015.1_MPIA_NFZ_2.0_genomic_WithFishTEDBv4.gtf Related to repository: https://github.com/BenayounLaboratory/Killifish_Transposon_Quantification

README — 基于RNA-seq数据的转座子（Transposable Element, TE）差异表达分析实验协议################################ ### 提供的参考文件 - 参考基因组序列、预测RNA序列及基因组注释文件（GCA_014300015.1；2020版基因组）。上述文件可公开获取于：https://www.ncbi.nlm.nih.gov/bioproject/PRJNA599375/，具体包含以下文件： GCA_014300015.1_MPIA_NFZ_2.0_genomic.fna GCA_014300015.1_MPIA_NFZ_2.0_genomic.gtf GCA_014300015.1_MPIA_NFZ_2.0_rna_from_genomic.fna - 弗氏假鳃鳉（Nothobranchius furzeri, N. furzeri）转座子的FishTEDB序列文件。该文件可从以下地址获取：http://www.fishtedb.org/project/species-detail?species=Nothobranchius+furzeri，文件名为：Nothobranchius_furzeri_FishTEDB_TEs.fa - 整合转座子序列与注释的修改版参考文件，适配两类分析方法： * 基于kallisto/转录组的分析方法：GCA_014300015.1_MPIA_NFZ_2.0_rna_from_genomic_WithFishTEDBv4.fasta * 基于STAR/基因组的分析方法： GCA_014300015.1_MPIA_NFZ_2.0_genomic_WithFishTEDBv4.fasta GCA_014300015.1_MPIA_NFZ_2.0_genomic_WithFishTEDBv4.gtf ### 关联代码仓库 https://github.com/BenayounLaboratory/Killifish_Transposon_Quantification

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2021-10-05

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